Glasgow East MP Natalie McGarry has been charged with fraud offences.
She had been under investigation by police after a pro-independence group reported a potential financial discrepancy in its accounts.
Ms McGarry, 35, had been one of the 56 SNP MPs elected in last year's general election.
She withdrew from the party whip when the allegations were made last November, and has been sitting as an independent MP.
The investigation into Ms McGarry centred on her involvement with Women for Independence (WFI), which was set up to campaign ahead of the referendum in September 2014.
WFI called in police after spotting apparent discrepancies between donations made to the organisation and its expenditure.
'Embezzlement of funds'
The allegations are believed to involve a five-figure sum of money.
It is understood the charges against Ms McGarry also relate to her involvement with the SNP Glasgow Regional Association.
Ms McGarry's lawyer, Aamer Anwar, told BBC Scotland that the MP had voluntarily attended Govan police station in Glasgow on Tuesday morning.
Mr Anwar added: "Following an interview she was charged with several alleged offences, including embezzlement of funds, breach of trust and an offence under the Scottish Independence Referendum Act 2013.
"She was released and there will now be a report to the procurator fiscal."
Ms McGarry has previously insisted there has been "no wrongdoing on her part".
Both Women for Independence and the SNP said they would not be commenting on the case.